It’s normal for a horse to overjump (or take extra effort) the next fence after hitting a rail or an awkward distance, but carrying it around course reads more like undiagnosed pain. The reason they get emotional is they are hurting doing the job as asked, but it really hurts when they have to exert their bodies and/or get out of a bad distance.
I would check his SI and back. When I hear the word ‘emotional’, it makes me suspect some degree of undiagnosed pain. YMMV.